Loading Library

library(knitr)
packageVersion("knitr")
## [1] '1.20'
library(energy)
packageVersion("energy")
## [1] '1.7.5'
library(broom)
packageVersion("broom")
## [1] '0.5.0'
library(plyr)
packageVersion("plyr")
## [1] '1.8.4'
library(kableExtra)
packageVersion("kableExtra")
## [1] '0.9.0'
library(foreach)
packageVersion("foreach")
## [1] '1.4.4'
library(doParallel)
## Loading required package: iterators
## Loading required package: parallel
packageVersion("doParallel")
## [1] '1.0.14'
set.seed(0)

Simulating MPEA Surrogate over the array.

load(file = "p53_curated.Rdata")
epsilon=1e-6
nominal_dcor_pvalues <- sapply(1:pathway_number, function(x) (epsilon+(sum(surrogate_dcor[[x]]>dcor_results[x])))/(1+num_simulation))
names(nominal_dcor_pvalues) <- names( pathway_collapsed)
head(sort(nominal_dcor_pvalues),10)
##                   REACTOME_GAB1_SIGNALOSOME 
##                                0.0000000001 
##                      REACTOME_PI_3K_CASCADE 
##                                0.0000000001 
##       REACTOME_PIP3_ACTIVATES_AKT_SIGNALING 
##                                0.0000000001 
##               GHANDHI_DIRECT_IRRADIATION_UP 
##                                0.0000000001 
##     QUINTENS_EMBRYONIC_BRAIN_RESPONSE_TO_IR 
##                                0.0000000001 
##                 MACAEVA_PBMC_RESPONSE_TO_IR 
##                                0.0000000001 
##                              KEGG_APOPTOSIS 
##                                0.0001000001 
##     REACTOME_PI3K_EVENTS_IN_ERBB4_SIGNALING 
##                                0.0001000001 
##    GAZDA_DIAMOND_BLACKFAN_ANEMIA_MYELOID_UP 
##                                0.0001000001 
## HOFMANN_MYELODYSPLASTIC_SYNDROM_LOW_RISK_UP 
##                                0.0002000001
dcor_significant_pathways_p.value <- sort(nominal_dcor_pvalues[nominal_dcor_pvalues <0.05])
length(dcor_significant_pathways_p.value)
## [1] 259
nominal_dcor_q_values <- p.adjust(nominal_dcor_pvalues , method = "fdr")
# nominal_dcor_q_values
nominal_dcor_q_values_under_25 <- sort(nominal_dcor_q_values[nominal_dcor_q_values<0.25])
length((nominal_dcor_q_values_under_25))
## [1] 102
nominal_dcor_q_values_under_25
##                                      REACTOME_GAB1_SIGNALOSOME 
##                                                   5.605000e-08 
##                                         REACTOME_PI_3K_CASCADE 
##                                                   5.605000e-08 
##                          REACTOME_PIP3_ACTIVATES_AKT_SIGNALING 
##                                                   5.605000e-08 
##                                  GHANDHI_DIRECT_IRRADIATION_UP 
##                                                   5.605000e-08 
##                        QUINTENS_EMBRYONIC_BRAIN_RESPONSE_TO_IR 
##                                                   5.605000e-08 
##                                    MACAEVA_PBMC_RESPONSE_TO_IR 
##                                                   5.605000e-08 
##                                                 KEGG_APOPTOSIS 
##                                                   3.736670e-02 
##                        REACTOME_PI3K_EVENTS_IN_ERBB4_SIGNALING 
##                                                   3.736670e-02 
##                       GAZDA_DIAMOND_BLACKFAN_ANEMIA_MYELOID_UP 
##                                                   3.736670e-02 
##                    HOFMANN_MYELODYSPLASTIC_SYNDROM_LOW_RISK_UP 
##                                                   6.726003e-02 
##                        REACTOME_PI3K_EVENTS_IN_ERBB2_SIGNALING 
##                                                   7.760772e-02 
##                   GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP 
##                                                   7.760772e-02 
##                                  SMIRNOV_RESPONSE_TO_IR_2HR_UP 
##                                                   7.760772e-02 
##                                           BIOCARTA_ATM_PATHWAY 
##                                                   8.407502e-02 
##                                  BIOCARTA_KERATINOCYTE_PATHWAY 
##                                                   8.407502e-02 
##                                                PID_FAS_PATHWAY 
##                                                   8.407502e-02 
##                     GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_UP 
##                                                   8.407502e-02 
##              TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_UP 
##                                                   8.407502e-02 
##                                       PROVENZANI_METASTASIS_UP 
##                                                   8.407502e-02 
##                                        MARZEC_IL2_SIGNALING_DN 
##                                                   8.407502e-02 
##                                            STEIN_ESRRA_TARGETS 
##                                                   9.608573e-02 
##                                                     MOOTHA_PGC 
##                                                   1.023522e-01 
##                                        WARTERS_IR_RESPONSE_5GY 
##                                                   1.023522e-01 
##                                           MATZUK_SPERMATOGONIA 
##                                                   1.034769e-01 
##                                    WARTERS_RESPONSE_TO_IR_SKIN 
##                                                   1.034769e-01 
##                                          NABA_SECRETED_FACTORS 
##                                                   1.034769e-01 
##                               VERHAAK_AML_WITH_NPM1_MUTATED_UP 
##                                                   1.080964e-01 
##                          BOYAULT_LIVER_CANCER_SUBCLASS_G123_DN 
##                                                   1.080964e-01 
##                       FISCHER_DIRECT_P53_TARGETS_META_ANALYSIS 
##                                                   1.275621e-01 
##                       CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5 
##                                                   1.345200e-01 
##                                                 PID_P73PATHWAY 
##                                                   1.518774e-01 
##                     MEISSNER_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3 
##                                                   1.528636e-01 
##                                            DURAND_STROMA_NS_UP 
##                                                   1.528636e-01 
##                    KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION 
##                                                   1.545162e-01 
##                                           BIOCARTA_FAS_PATHWAY 
##                                                   1.545162e-01 
##                        BARRIER_CANCER_RELAPSE_NORMAL_SAMPLE_UP 
##                                                   1.545162e-01 
##                                          MARKS_HDAC_TARGETS_UP 
##                                                   1.545162e-01 
##                                          WANG_CLIM2_TARGETS_DN 
##                                                   1.681500e-01 
##                                   AMIT_EGF_RESPONSE_120_MCF10A 
##                                                   1.681500e-01 
##                                         KANNAN_TP53_TARGETS_UP 
##                                                   1.681500e-01 
##                                         GENTILE_UV_LOW_DOSE_UP 
##                                                   1.681500e-01 
##                                         STEIN_ESRRA_TARGETS_UP 
##                                                   1.681500e-01 
##                              HELLER_SILENCED_BY_METHYLATION_DN 
##                                                   1.720605e-01 
##                                  BIOCARTA_MITOCHONDRIA_PATHWAY 
##                                                   1.757932e-01 
##                                        SESTO_RESPONSE_TO_UV_C0 
##                                                   1.793600e-01 
##                    MAGRANGEAS_MULTIPLE_MYELOMA_IGLL_VS_IGLK_UP 
##                                                   1.900826e-01 
##                                            PID_HIV_NEF_PATHWAY 
##                                                   2.004865e-01 
##                                         LIU_PROSTATE_CANCER_UP 
##                                                   2.004865e-01 
##                       SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_DN 
##                                                   2.004865e-01 
##                                 MANN_RESPONSE_TO_AMIFOSTINE_UP 
##                                                   2.004865e-01 
##                            TSAI_RESPONSE_TO_IONIZING_RADIATION 
##                                                   2.004865e-01 
##                                      VILIMAS_NOTCH1_TARGETS_DN 
##                                                   2.004865e-01 
##                                      CORRE_MULTIPLE_MYELOMA_UP 
##                                                   2.030491e-01 
##                                             SA_CASPASE_CASCADE 
##                                                   2.065000e-01 
##                                   HAMAI_APOPTOSIS_VIA_TRAIL_DN 
##                                                   2.065000e-01 
##                                            WU_HBX_TARGETS_2_UP 
##                                                   2.065000e-01 
##                                          SAGIV_CD24_TARGETS_DN 
##                                                   2.065000e-01 
##                                       DUTTA_APOPTOSIS_VIA_NFKB 
##                                                   2.087379e-01 
##                                      BIOCARTA_CERAMIDE_PATHWAY 
##                                                   2.109000e-01 
##                 SENGUPTA_NASOPHARYNGEAL_CARCINOMA_WITH_LMP1_UP 
##                                                   2.148583e-01 
##     GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_TURQUOISE_UP 
##                                                   2.148583e-01 
##                                         GOZGIT_ESR1_TARGETS_DN 
##                                                   2.148583e-01 
##                                KERLEY_RESPONSE_TO_CISPLATIN_UP 
##                                                   2.148583e-01 
##                               KAN_RESPONSE_TO_ARSENIC_TRIOXIDE 
##                                                   2.148583e-01 
##                                 MAHADEVAN_RESPONSE_TO_MP470_DN 
##                                                   2.148583e-01 
##                               WANG_METHYLATED_IN_BREAST_CANCER 
##                                                   2.148583e-01 
##                                             NAKAJIMA_MAST_CELL 
##                                                   2.148583e-01 
##                                           LIAN_LIPA_TARGETS_6M 
##                                                   2.148583e-01 
##                                           LIAN_LIPA_TARGETS_3M 
##                                                   2.148583e-01 
##                                  COATES_MACROPHAGE_M1_VS_M2_DN 
##                                                   2.148583e-01 
##                          MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_UP 
##                                                   2.148583e-01 
##                                  SMIRNOV_RESPONSE_TO_IR_6HR_UP 
##                                                   2.148583e-01 
##            SATO_SILENCED_BY_DEACETYLATION_IN_PANCREATIC_CANCER 
##                                                   2.257356e-01 
##                          KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS 
##                                                   2.317743e-01 
##                                          KYNG_RESPONSE_TO_H2O2 
##                                                   2.331680e-01 
##                               JI_METASTASIS_REPRESSED_BY_STK11 
##                                                   2.389500e-01 
##                          MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_UP 
##                                                   2.445818e-01 
##                                        KIM_WT1_TARGETS_12HR_UP 
##                                                   2.453012e-01 
##                WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_UP 
##                                                   2.453012e-01 
##                            CHUANG_OXIDATIVE_STRESS_RESPONSE_UP 
##                                                   2.453012e-01 
##                                             VALK_AML_CLUSTER_7 
##                                                   2.453012e-01 
##                                POOLA_INVASIVE_BREAST_CANCER_UP 
##                                                   2.453012e-01 
##                                      WHITFIELD_CELL_CYCLE_M_G1 
##                                                   2.453012e-01 
##                                         HOELZEL_NF1_TARGETS_UP 
##                                                   2.453012e-01 
##                                               WANG_TNF_TARGETS 
##                                                   2.453012e-01 
##               REACTOME_FORMATION_OF_INCISION_COMPLEX_IN_GG_NER 
##                                                   2.461577e-01 
## TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINED_IN_MONOCYTE_UP 
##                                                   2.461577e-01 
##                           LENAOUR_DENDRITIC_CELL_MATURATION_UP 
##                                                   2.461577e-01 
##                   CHIARETTI_ACUTE_LYMPHOBLASTIC_LEUKEMIA_ZAP70 
##                                                   2.461577e-01 
##                                        WANG_SMARCE1_TARGETS_DN 
##                                                   2.461577e-01 
##                                     WALLACE_PROSTATE_CANCER_UP 
##                                                   2.461577e-01 
##                                            RUIZ_TNC_TARGETS_UP 
##                                                   2.461577e-01 
##                    MIKKELSEN_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3 
##                                                   2.461577e-01 
##                                      KASLER_HDAC7_TARGETS_1_UP 
##                                                   2.461577e-01 
##                           PURBEY_TARGETS_OF_CTBP1_NOT_SATB1_UP 
##                                                   2.461577e-01 
##                                     KATSANOU_ELAVL1_TARGETS_UP 
##                                                   2.461577e-01 
##                                        KRIEG_HYPOXIA_VIA_KDM3A 
##                                                   2.461577e-01 
##                                              PID_TAP63_PATHWAY 
##                                                   2.472794e-01 
##                            APPIERTO_RESPONSE_TO_FENRETINIDE_UP 
##                                                   2.472794e-01 
##                                    MOHANKUMAR_HOXA1_TARGETS_DN 
##                                                   2.472794e-01 
##                                     AMIT_EGF_RESPONSE_120_HELA 
##                                                   2.472794e-01 
##                                            WU_HBX_TARGETS_1_UP 
##                                                   2.472794e-01

GSEA signifcanct pathways p-value and Q-value

nrow(gsea_results_significant)
## [1] 164
length(rownames(gsea_results_significant[gsea_results_significant$FDR.q.val<0.25,]))
## [1] 10

Identifying the pathways deemed significant in both GSEA and MPEA

Mutually_identified_in_GSEA_dcor <- intersect(names(dcor_significant_pathways_p.value), rownames(gsea_results_significant))

Mutually_identified_in_GSEA_dcor
##  [1] "REACTOME_GAB1_SIGNALOSOME"                 
##  [2] "REACTOME_PIP3_ACTIVATES_AKT_SIGNALING"     
##  [3] "QUINTENS_EMBRYONIC_BRAIN_RESPONSE_TO_IR"   
##  [4] "MACAEVA_PBMC_RESPONSE_TO_IR"               
##  [5] "SMIRNOV_RESPONSE_TO_IR_2HR_UP"             
##  [6] "WARTERS_IR_RESPONSE_5GY"                   
##  [7] "MATZUK_SPERMATOGONIA"                      
##  [8] "WARTERS_RESPONSE_TO_IR_SKIN"               
##  [9] "NABA_SECRETED_FACTORS"                     
## [10] "FISCHER_DIRECT_P53_TARGETS_META_ANALYSIS"  
## [11] "PID_P73PATHWAY"                            
## [12] "KANNAN_TP53_TARGETS_UP"                    
## [13] "GENTILE_UV_LOW_DOSE_UP"                    
## [14] "MANN_RESPONSE_TO_AMIFOSTINE_UP"            
## [15] "VILIMAS_NOTCH1_TARGETS_DN"                 
## [16] "LIAN_LIPA_TARGETS_6M"                      
## [17] "SMIRNOV_RESPONSE_TO_IR_6HR_UP"             
## [18] "KERLEY_RESPONSE_TO_CISPLATIN_UP"           
## [19] "LIAN_LIPA_TARGETS_3M"                      
## [20] "PID_TAP63_PATHWAY"                         
## [21] "RAMALHO_STEMNESS_DN"                       
## [22] "MCLACHLAN_DENTAL_CARIES_UP"                
## [23] "PID_P53_DOWNSTREAM_PATHWAY"                
## [24] "BIOCARTA_CHEMICAL_PATHWAY"                 
## [25] "LABBE_TGFB1_TARGETS_DN"                    
## [26] "ABE_VEGFA_TARGETS_2HR"                     
## [27] "BIOCARTA_CK1_PATHWAY"                      
## [28] "CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_UP"    
## [29] "FOSTER_KDM1A_TARGETS_UP"                   
## [30] "SU_PANCREAS"                               
## [31] "REACTOME_AMINE_LIGAND_BINDING_RECEPTORS"   
## [32] "MCMURRAY_TP53_HRAS_COOPERATION_RESPONSE_DN"
## [33] "HASLINGER_B_CLL_WITH_CHROMOSOME_12_TRISOMY"
## [34] "ROYLANCE_BREAST_CANCER_16Q_COPY_NUMBER_UP" 
## [35] "EBAUER_TARGETS_OF_PAX3_FOXO1_FUSION_DN"
Mutually_identified_in_GSEA_dcor_fdr <- intersect(names(nominal_dcor_q_values_under_25),rownames(gsea_results_significant[gsea_results_significant$FDR.q.val<0.25,]))
length(Mutually_identified_in_GSEA_dcor_fdr)
## [1] 5

Identifying the pathways significant in MPEA not in GSEA

Significant_in_dcor_not_in_GSEA <- setdiff(names(dcor_significant_pathways_p.value),Mutually_identified_in_GSEA_dcor)
pvalue_of_disparities <- rbind(dcor_significant_pathways_p.value[Significant_in_dcor_not_in_GSEA],gsea_results[Significant_in_dcor_not_in_GSEA,]$NOM.p.val)
rownames(pvalue_of_disparities) <- c("MPEA","GSEA")
pvalue_of_disparities%>%
  kable("html", digits = 4, longtable = TRUE) %>%
  kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
  row_spec(0, angle = -0)
REACTOME_PI_3K_CASCADE GHANDHI_DIRECT_IRRADIATION_UP KEGG_APOPTOSIS REACTOME_PI3K_EVENTS_IN_ERBB4_SIGNALING GAZDA_DIAMOND_BLACKFAN_ANEMIA_MYELOID_UP HOFMANN_MYELODYSPLASTIC_SYNDROM_LOW_RISK_UP REACTOME_PI3K_EVENTS_IN_ERBB2_SIGNALING GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP BIOCARTA_KERATINOCYTE_PATHWAY MARZEC_IL2_SIGNALING_DN BIOCARTA_ATM_PATHWAY PID_FAS_PATHWAY GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_UP TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_UP PROVENZANI_METASTASIS_UP STEIN_ESRRA_TARGETS MOOTHA_PGC VERHAAK_AML_WITH_NPM1_MUTATED_UP BOYAULT_LIVER_CANCER_SUBCLASS_G123_DN CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5 MEISSNER_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3 DURAND_STROMA_NS_UP KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION BIOCARTA_FAS_PATHWAY BARRIER_CANCER_RELAPSE_NORMAL_SAMPLE_UP MARKS_HDAC_TARGETS_UP WANG_CLIM2_TARGETS_DN AMIT_EGF_RESPONSE_120_MCF10A STEIN_ESRRA_TARGETS_UP HELLER_SILENCED_BY_METHYLATION_DN BIOCARTA_MITOCHONDRIA_PATHWAY SESTO_RESPONSE_TO_UV_C0 MAGRANGEAS_MULTIPLE_MYELOMA_IGLL_VS_IGLK_UP SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_DN LIU_PROSTATE_CANCER_UP TSAI_RESPONSE_TO_IONIZING_RADIATION PID_HIV_NEF_PATHWAY CORRE_MULTIPLE_MYELOMA_UP SA_CASPASE_CASCADE HAMAI_APOPTOSIS_VIA_TRAIL_DN WU_HBX_TARGETS_2_UP SAGIV_CD24_TARGETS_DN DUTTA_APOPTOSIS_VIA_NFKB BIOCARTA_CERAMIDE_PATHWAY NAKAJIMA_MAST_CELL WANG_METHYLATED_IN_BREAST_CANCER GOZGIT_ESR1_TARGETS_DN KAN_RESPONSE_TO_ARSENIC_TRIOXIDE SENGUPTA_NASOPHARYNGEAL_CARCINOMA_WITH_LMP1_UP GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_TURQUOISE_UP MAHADEVAN_RESPONSE_TO_MP470_DN COATES_MACROPHAGE_M1_VS_M2_DN MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_UP SATO_SILENCED_BY_DEACETYLATION_IN_PANCREATIC_CANCER KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS KYNG_RESPONSE_TO_H2O2 JI_METASTASIS_REPRESSED_BY_STK11 MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_UP HOELZEL_NF1_TARGETS_UP POOLA_INVASIVE_BREAST_CANCER_UP KIM_WT1_TARGETS_12HR_UP CHUANG_OXIDATIVE_STRESS_RESPONSE_UP WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_UP WHITFIELD_CELL_CYCLE_M_G1 VALK_AML_CLUSTER_7 WANG_TNF_TARGETS WANG_SMARCE1_TARGETS_DN MIKKELSEN_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3 RUIZ_TNC_TARGETS_UP TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINED_IN_MONOCYTE_UP LENAOUR_DENDRITIC_CELL_MATURATION_UP KATSANOU_ELAVL1_TARGETS_UP REACTOME_FORMATION_OF_INCISION_COMPLEX_IN_GG_NER WALLACE_PROSTATE_CANCER_UP KASLER_HDAC7_TARGETS_1_UP CHIARETTI_ACUTE_LYMPHOBLASTIC_LEUKEMIA_ZAP70 PURBEY_TARGETS_OF_CTBP1_NOT_SATB1_UP KRIEG_HYPOXIA_VIA_KDM3A MOHANKUMAR_HOXA1_TARGETS_DN AMIT_EGF_RESPONSE_120_HELA WU_HBX_TARGETS_1_UP APPIERTO_RESPONSE_TO_FENRETINIDE_UP REACTOME_INTRINSIC_PATHWAY_FOR_APOPTOSIS KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP BIOCARTA_BAD_PATHWAY BOYLAN_MULTIPLE_MYELOMA_C_CLUSTER_UP MENSSEN_MYC_TARGETS REACTOME_VOLTAGE_GATED_POTASSIUM_CHANNELS PRAMOONJAGO_SOX4_TARGETS_UP SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_UP TENEDINI_MEGAKARYOCYTE_MARKERS BIOCARTA_RAC1_PATHWAY KANG_IMMORTALIZED_BY_TERT_UP KIM_MYCN_AMPLIFICATION_TARGETS_UP PLASARI_TGFB1_SIGNALING_VIA_NFIC_10HR_UP PACHER_TARGETS_OF_IGF1_AND_IGF2_UP LIU_SMARCA4_TARGETS RIGGI_EWING_SARCOMA_PROGENITOR_UP REACTOME_POTASSIUM_CHANNELS SHIN_B_CELL_LYMPHOMA_CLUSTER_7 WINZEN_DEGRADED_VIA_KHSRP REACTOME_P53_DEPENDENT_G1_DNA_DAMAGE_RESPONSE BASAKI_YBX1_TARGETS_DN CONCANNON_APOPTOSIS_BY_EPOXOMICIN_UP BILD_HRAS_ONCOGENIC_SIGNATURE OUILLETTE_CLL_13Q14_DELETION_UP REACTOME_SCFSKP2_MEDIATED_DEGRADATION_OF_P27_P21 HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_4NM_UP REACTOME_CYCLIN_E_ASSOCIATED_EVENTS_DURING_G1_S_TRANSITION_ TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_8D_UP LAU_APOPTOSIS_CDKN2A_UP GALLUZZI_PREVENT_MITOCHONDIAL_PERMEABILIZATION KEGG_AMYOTROPHIC_LATERAL_SCLEROSIS_ALS SEKI_INFLAMMATORY_RESPONSE_LPS_UP HOFMANN_MYELODYSPLASTIC_SYNDROM_RISK_UP REACTOME_CELL_CYCLE_CHECKPOINTS BOYAULT_LIVER_CANCER_SUBCLASS_G1_UP REACTOME_SIGNALING_BY_SCF_KIT REACTOME_ORC1_REMOVAL_FROM_CHROMATIN HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_DN ZHANG_PROLIFERATING_VS_QUIESCENT REACTOME_DOWNSTREAM_SIGNAL_TRANSDUCTION KEGG_EPITHELIAL_CELL_SIGNALING_IN_HELICOBACTER_PYLORI_INFECTION REACTOME_SYNTHESIS_OF_DNA REACTOME_DNA_REPLICATION BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_UP BHAT_ESR1_TARGETS_VIA_AKT1_UP KEGG_PRION_DISEASES REACTOME_MITOTIC_G2_G2_M_PHASES NAGASHIMA_NRG1_SIGNALING_UP PID_CDC42_PATHWAY GRADE_COLON_AND_RECTAL_CANCER_UP MIKKELSEN_ES_ICP_WITH_H3K27ME3 IIZUKA_LIVER_CANCER_PROGRESSION_L0_L1_DN MOOTHA_HUMAN_MITODB_6_2002 WANG_ESOPHAGUS_CANCER_VS_NORMAL_DN SEITZ_NEOPLASTIC_TRANSFORMATION_BY_8P_DELETION_DN DOANE_BREAST_CANCER_ESR1_UP KOKKINAKIS_METHIONINE_DEPRIVATION_96HR_DN LEE_NEURAL_CREST_STEM_CELL_DN GYORFFY_DOXORUBICIN_RESISTANCE GOLUB_ALL_VS_AML_DN PID_E2F_PATHWAY WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_WITH_H4K20ME1_MARK MORI_SMALL_PRE_BII_LYMPHOCYTE_DN VALK_AML_CLUSTER_3 REACTOME_G1_S_TRANSITION KEGG_INOSITOL_PHOSPHATE_METABOLISM BIOCARTA_MYOSIN_PATHWAY BIOCARTA_ACTINY_PATHWAY REACTOME_CDK_MEDIATED_PHOSPHORYLATION_AND_REMOVAL_OF_CDC6 REACTOME_REGULATION_OF_MITOTIC_CELL_CYCLE MULLIGHAN_NPM1_SIGNATURE_3_UP CHEOK_RESPONSE_TO_MERCAPTOPURINE_DN MIKKELSEN_ES_ICP_WITH_H3K4ME3 HOFFMANN_IMMATURE_TO_MATURE_B_LYMPHOCYTE_UP REACTOME_MITOTIC_M_M_G1_PHASES BENPORATH_CYCLING_GENES DARWICHE_SKIN_TUMOR_PROMOTER_DN VECCHI_GASTRIC_CANCER_EARLY_UP ELVIDGE_HYPOXIA_BY_DMOG_UP COATES_MACROPHAGE_M1_VS_M2_UP NAKAMURA_ADIPOGENESIS_LATE_DN YAMAZAKI_TCEB3_TARGETS_DN HOFFMANN_PRE_BI_TO_LARGE_PRE_BII_LYMPHOCYTE_UP VARELA_ZMPSTE24_TARGETS_UP REACTOME_G0_AND_EARLY_G1 HELLER_HDAC_TARGETS_DN HOEBEKE_LYMPHOID_STEM_CELL_DN ELVIDGE_HYPOXIA_UP LANDIS_ERBB2_BREAST_TUMORS_65_UP ACEVEDO_FGFR1_TARGETS_IN_PROSTATE_CANCER_MODEL_UP HASLINGER_B_CLL_WITH_MUTATED_VH_GENES SPIRA_SMOKERS_LUNG_CANCER_UP BIOCARTA_HIVNEF_PATHWAY GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_UP MOOTHA_GLUCONEOGENESIS MIKKELSEN_IPS_ICP_WITH_H3K27ME3 PID_RAC1_PATHWAY PID_RHODOPSIN_PATHWAY GRADE_COLON_AND_RECTAL_CANCER_DN SAKAI_TUMOR_INFILTRATING_MONOCYTES_DN BIOCARTA_CALCINEURIN_PATHWAY KIM_LIVER_CANCER_POOR_SURVIVAL_DN PROVENZANI_METASTASIS_DN SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM6 SHIN_B_CELL_LYMPHOMA_CLUSTER_8 PID_BMP_PATHWAY REACTOME_M_G1_TRANSITION KRIEG_KDM3A_TARGETS_NOT_HYPOXIA FERNANDEZ_BOUND_BY_MYC GALINDO_IMMUNE_RESPONSE_TO_ENTEROTOXIN REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS KAUFFMANN_DNA_REPLICATION_GENES CAFFAREL_RESPONSE_TO_THC_24HR_5_UP GROSS_HIF1A_TARGETS_DN LABBE_WNT3A_TARGETS_DN OHGUCHI_LIVER_HNF4A_TARGETS_UP VIETOR_IFRD1_TARGETS LEE_LIVER_CANCER_SURVIVAL_UP TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINDED_IN_ERYTHROCYTE_UP GRAHAM_CML_QUIESCENT_VS_NORMAL_QUIESCENT_DN SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_UP MARCHINI_TRABECTEDIN_RESISTANCE_DN ROSS_AML_OF_FAB_M7_TYPE WHITFIELD_CELL_CYCLE_LITERATURE KEGG_NOD_LIKE_RECEPTOR_SIGNALING_PATHWAY REACTOME_PI_METABOLISM CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_3 AGUIRRE_PANCREATIC_CANCER_COPY_NUMBER_DN VALK_AML_CLUSTER_16 WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_8D FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_OK_VS_DONOR_DN ALONSO_METASTASIS_NEURAL_UP CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_CDC25_DN KEGG_OOCYTE_MEIOSIS HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_1_DN REACTOME_METABOLISM_OF_NUCLEOTIDES FARMER_BREAST_CANCER_BASAL_VS_LULMINAL ONDER_CDH1_TARGETS_1_UP TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_HSC_UP KEGG_NOTCH_SIGNALING_PATHWAY SMID_BREAST_CANCER_LUMINAL_B_UP REACTOME_GLUCONEOGENESIS
MPEA 0.0000 0.0000 0.0001 0.0001 0.0001 0.0002 0.0003 0.0003 0.0004 0.0004 0.0005 0.0005 0.0005 0.0005 0.0005 0.0006 0.0007 0.0009 0.0009 0.0012 0.0015 0.0015 0.0016 0.0017 0.0017 0.0017 0.0020 0.0020 0.0021 0.0022 0.0023 0.0024 0.0026 0.0029 0.0030 0.0030 0.0031 0.0032 0.0034 0.0035 0.0035 0.0035 0.0036 0.0037 0.0040 0.0041 0.0043 0.0043 0.0045 0.0046 0.0046 0.0046 0.0046 0.0049 0.0051 0.0052 0.0054 0.0056 0.0057 0.0058 0.0059 0.0060 0.0061 0.0061 0.0062 0.0062 0.0063 0.0065 0.0066 0.0067 0.0068 0.0069 0.007 0.0070 0.0070 0.0071 0.0071 0.0071 0.0074 0.0074 0.0074 0.0075 0.0078 0.0080 0.0082 0.0082 0.0083 0.0084 0.0084 0.0086 0.0087 0.0088 0.0093 0.0094 0.0094 0.0096 0.0098 0.0098 0.0100 0.0103 0.0106 0.0109 0.0112 0.0115 0.0115 0.0115 0.0116 0.0118 0.0123 0.0123 0.0124 0.0127 0.0131 0.0131 0.0133 0.0139 0.0143 0.0144 0.0145 0.0148 0.0153 0.0163 0.0170 0.0170 0.0176 0.0178 0.0179 0.0182 0.0193 0.0193 0.0197 0.0198 0.0202 0.0206 0.0206 0.0208 0.0208 0.0209 0.0210 0.0216 0.0218 0.0224 0.0232 0.0237 0.0240 0.0241 0.0242 0.0247 0.0248 0.0248 0.0249 0.0251 0.0255 0.0256 0.026 0.0261 0.0265 0.0269 0.0271 0.0273 0.0275 0.0275 0.0275 0.0285 0.0289 0.0290 0.0291 0.0293 0.0295 0.0296 0.0302 0.0309 0.0312 0.0318 0.0326 0.0334 0.0336 0.0337 0.0340 0.0341 0.0342 0.0348 0.0349 0.0354 0.0360 0.0362 0.0367 0.0368 0.0371 0.0371 0.0374 0.0375 0.0381 0.0393 0.0403 0.0408 0.0409 0.0410 0.0413 0.0413 0.0420 0.0426 0.0426 0.0426 0.0427 0.0428 0.0432 0.0433 0.0438 0.0440 0.0446 0.0448 0.0454 0.0455 0.0458 0.0466 0.0470 0.0471 0.0485 0.0485 0.0487 0.0490 0.0490 0.0491
GSEA 0.2321 0.2551 0.5364 0.1674 0.0769 0.1869 0.2662 0.9398 0.4801 0.9227 0.1736 0.4680 0.0699 0.6484 0.3756 0.4410 0.9450 0.6571 0.1494 0.2531 0.6642 0.1983 0.0507 0.6530 0.6566 0.3252 0.1663 0.5556 0.7281 0.9698 0.3139 0.5696 0.8706 0.5194 0.6125 0.2661 0.4794 0.6246 0.6592 0.0746 0.4670 0.5405 0.0609 0.3425 0.4614 0.5593 0.7892 0.7223 0.2194 0.3561 0.7326 0.3593 0.4448 0.9314 0.5144 0.9074 0.6964 0.5526 0.7301 0.6568 0.9545 0.0754 0.3996 0.5262 0.6354 0.7523 0.4209 0.2435 0.9976 0.9686 0.0508 0.3245 0.474 0.7941 0.2397 0.3301 0.3767 0.7842 0.7064 0.5863 0.3274 0.7107 0.0522 0.5484 0.0635 0.4479 0.7983 0.3642 0.4953 0.5367 0.9282 0.3364 0.5355 0.3342 0.8603 0.9663 0.6195 0.9113 0.3319 0.4894 0.8922 0.7238 0.8142 0.9013 0.9346 0.1835 0.7419 0.3170 0.7361 0.6043 0.7462 0.3943 0.3124 0.7540 0.9412 0.4349 0.4401 0.5251 0.6863 0.1444 0.2260 0.1474 0.5295 0.5717 0.4133 0.3484 0.8831 0.2797 0.2906 0.3210 0.9206 0.5824 0.4437 0.5412 0.7146 0.9611 0.0595 0.6554 0.3117 0.5828 0.8597 0.3410 0.5491 0.6893 0.3177 0.6101 0.5585 0.5199 0.6196 0.6891 0.3209 0.2844 0.4840 0.5017 0.500 0.2225 0.2490 0.3605 0.0549 0.1874 0.2559 0.5741 0.8265 0.2085 0.0940 0.0659 0.4388 0.3587 0.7762 0.1821 0.0916 0.7786 0.2547 0.3803 0.4729 0.2368 0.6509 0.3236 0.4141 0.3957 0.6731 0.5282 0.1843 0.2105 0.3824 0.6667 0.6115 0.0833 0.3622 0.6096 0.6126 0.4313 0.1454 0.7944 0.3812 0.1238 0.1708 0.8321 0.4260 0.3101 0.4203 0.3835 0.7438 0.9955 0.9107 0.4195 0.2495 0.3679 0.1652 0.7172 0.3357 0.3618 0.0756 0.6831 0.7266 0.3247 0.6114 0.9388 0.2954 0.4255 0.6801 0.3309 0.7488 0.7050

Identifying the pathways significant in GSEA not in MPEA

Significant_in_GSEA_not_in_dcor <- setdiff(rownames(gsea_results_significant),Mutually_identified_in_GSEA_dcor)
pvalue_of_disparities <- rbind(nominal_dcor_pvalues[Significant_in_GSEA_not_in_dcor],gsea_results[Significant_in_GSEA_not_in_dcor,]$NOM.p.val)
rownames(pvalue_of_disparities) <- c("MPEA","GSEA")
pvalue_of_disparities %>%
  kable("html", digits = 4, longtable = TRUE) %>%
  kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
  row_spec(0, angle = -0)
AMUNDSON_DNA_DAMAGE_RESPONSE_TP53 BIOCARTA_P53_PATHWAY WILENSKY_RESPONSE_TO_DARAPLADIB LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN REACTOME_PEPTIDE_LIGAND_BINDING_RECEPTORS BIOCARTA_P53HYPOXIA_PATHWAY REACTOME_PHASE_II_CONJUGATION ODONNELL_METASTASIS_UP REACTOME_CLASS_A1_RHODOPSIN_LIKE_RECEPTORS NIKOLSKY_BREAST_CANCER_16Q24_AMPLICON MEISSNER_NPC_HCP_WITH_H3K4ME2_AND_H3K27ME3 NIELSEN_GIST_AND_SYNOVIAL_SARCOMA_DN REACTOME_EFFECTS_OF_PIP2_HYDROLYSIS REACTOME_LIPOPROTEIN_METABOLISM VALK_AML_CLUSTER_13 KEGG_P53_SIGNALING_PATHWAY BIOCARTA_CYTOKINE_PATHWAY KEGG_CALCIUM_SIGNALING_PATHWAY VANDESLUIS_COMMD1_TARGETS_GROUP_4_UP REACTOME_CA_DEPENDENT_EVENTS CHEN_ETV5_TARGETS_SERTOLI ONGUSAHA_TP53_TARGETS TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_DN REACTOME_REGULATION_OF_IFNA_SIGNALING BIOCARTA_NO2IL12_PATHWAY BIOCARTA_INFLAM_PATHWAY REACTOME_CHEMOKINE_RECEPTORS_BIND_CHEMOKINES REACTOME_G_ALPHA_I_SIGNALLING_EVENTS REACTOME_PLC_BETA_MEDIATED_EVENTS REACTOME_GPCR_LIGAND_BINDING REACTOME_DAG_AND_IP3_SIGNALING CEBALLOS_TARGETS_OF_TP53_AND_MYC_DN YAUCH_HEDGEHOG_SIGNALING_PARACRINE_DN PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_DN KEGG_OLFACTORY_TRANSDUCTION MIKKELSEN_MCV6_ICP_WITH_H3K27ME3 PID_NCADHERIN_PATHWAY FIGUEROA_AML_METHYLATION_CLUSTER_5_DN REACTOME_G_ALPHA_Q_SIGNALLING_EVENTS BREDEMEYER_RAG_SIGNALING_VIA_ATM_NOT_VIA_NFKB_UP THEODOROU_MAMMARY_TUMORIGENESIS HOLLEMAN_VINCRISTINE_RESISTANCE_ALL_UP NIELSEN_SYNOVIAL_SARCOMA_DN REACTOME_NITRIC_OXIDE_STIMULATES_GUANYLATE_CYCLASE REACTOME_PHOSPHOLIPASE_C_MEDIATED_CASCADE MARSON_FOXP3_TARGETS_DN REACTOME_GPCR_DOWNSTREAM_SIGNALING GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLACK_UP REACTOME_LYSOSOME_VESICLE_BIOGENESIS KAMMINGA_SENESCENCE ODONNELL_TFRC_TARGETS_UP GAVIN_FOXP3_TARGETS_CLUSTER_T4 DARWICHE_PAPILLOMA_PROGRESSION_RISK YAMASHITA_LIVER_CANCER_STEM_CELL_DN PEDRIOLI_MIR31_TARGETS_DN BENPORATH_PRC2_TARGETS HESS_TARGETS_OF_HOXA9_AND_MEIS1_DN SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A12 OHGUCHI_LIVER_HNF4A_TARGETS_DN MA_MYELOID_DIFFERENTIATION_DN ICHIBA_GRAFT_VERSUS_HOST_DISEASE_35D_DN REACTOME_SIGNALING_BY_GPCR PID_INTEGRIN_CS_PATHWAY FLORIO_NEOCORTEX_BASAL_RADIAL_GLIA_UP BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_TRANS XU_HGF_TARGETS_REPRESSED_BY_AKT1_DN ONO_FOXP3_TARGETS_DN KEGG_TYPE_I_DIABETES_MELLITUS HOQUE_METHYLATED_IN_CANCER ZHANG_GATA6_TARGETS_DN KONDO_PROSTATE_CANCER_WITH_H3K27ME3 PID_IL4_2PATHWAY MIKKELSEN_NPC_HCP_WITH_H3K27ME3 REN_ALVEOLAR_RHABDOMYOSARCOMA_UP RIZKI_TUMOR_INVASIVENESS_3D_UP TAYLOR_METHYLATED_IN_ACUTE_LYMPHOBLASTIC_LEUKEMIA BROWNE_HCMV_INFECTION_2HR_DN ANDERSEN_CHOLANGIOCARCINOMA_CLASS2 REACTOME_ASPARAGINE_N_LINKED_GLYCOSYLATION MORI_PLASMA_CELL_UP WANG_RESPONSE_TO_BEXAROTENE_DN FAELT_B_CLL_WITH_VH3_21_DN TSENG_ADIPOGENIC_POTENTIAL_UP KEGG_N_GLYCAN_BIOSYNTHESIS WELCSH_BRCA1_TARGETS_UP PID_WNT_NONCANONICAL_PATHWAY HINATA_NFKB_TARGETS_KERATINOCYTE_DN REACTOME_GRB2_EVENTS_IN_ERBB2_SIGNALING BIOCARTA_RAS_PATHWAY RODRIGUES_NTN1_TARGETS_DN PID_EPHB_FWD_PATHWAY BURTON_ADIPOGENESIS_11 REACTOME_NOTCH1_INTRACELLULAR_DOMAIN_REGULATES_TRANSCRIPTION REACTOME_PEROXISOMAL_LIPID_METABOLISM NUYTTEN_NIPP1_TARGETS_DN BENPORATH_ES_CORE_NINE_CORRELATED JI_RESPONSE_TO_FSH_DN DORSAM_HOXA9_TARGETS_UP PID_HDAC_CLASSI_PATHWAY BIOCARTA_IGF1_PATHWAY REACTOME_PROLONGED_ERK_ACTIVATION_EVENTS PID_HDAC_CLASSII_PATHWAY AMIT_SERUM_RESPONSE_120_MCF10A WINTER_HYPOXIA_UP DACOSTA_UV_RESPONSE_VIA_ERCC3_TTD_DN BARIS_THYROID_CANCER_DN LANDIS_ERBB2_BREAST_TUMORS_324_UP SEIDEN_MET_SIGNALING TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_DUCTAL_NORMAL_DN REACTOME_SHC1_EVENTS_IN_ERBB4_SIGNALING LEE_AGING_MUSCLE_DN BIOCARTA_FMLP_PATHWAY BIOCARTA_NGF_PATHWAY REACTOME_ENOS_ACTIVATION_AND_REGULATION GROSS_HYPOXIA_VIA_HIF1A_DN STONER_ESOPHAGEAL_CARCINOGENESIS_UP BIOCARTA_BCR_PATHWAY PID_AVB3_OPN_PATHWAY SA_B_CELL_RECEPTOR_COMPLEXES PUIFFE_INVASION_INHIBITED_BY_ASCITES_UP TRACEY_RESISTANCE_TO_IFNA2_DN KAAB_FAILED_HEART_ATRIUM_DN WANG_TUMOR_INVASIVENESS_DN FORTSCHEGGER_PHF8_TARGETS_DN SESTO_RESPONSE_TO_UV_C7 WANG_HCP_PROSTATE_CANCER REACTOME_CTLA4_INHIBITORY_SIGNALING KYNG_DNA_DAMAGE_BY_GAMMA_AND_UV_RADIATION GOTZMANN_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_DN
MPEA 0.0518 0.1474 0.4621 0.9999 0.1764 0.3714 0.8323 0.9955 0.2203 0.0862 0.4539 0.3552 0.5429 0.2481 0.2298 0.2731 0.9646 0.7855 0.6565 0.1327 0.0543 0.2684 0.2133 0.7143 0.8424 0.6721 0.2328 0.7396 0.2266 0.6491 0.1319 0.5296 0.9984 0.082 0.9686 0.6609 0.2062 0.1085 0.2098 0.6668 0.0885 0.3777 0.4788 0.2443 0.1472 0.3104 0.7955 0.1270 0.5092 0.9549 0.5115 0.6431 0.6050 0.9832 0.3554 0.0606 0.6760 0.7193 0.6484 0.4076 0.6235 0.3036 0.6401 0.9895 0.1885 0.5003 0.4317 0.5914 0.7320 0.3322 0.9974 0.7264 0.9087 0.3551 0.4912 0.9877 0.5798 0.6062 0.3490 0.2290 0.4834 0.2462 0.7869 0.1232 0.5075 0.6393 0.6424 0.4665 0.3850 0.9282 0.5128 0.2434 0.4162 0.2025 0.6619 0.6208 0.8154 0.8192 0.7275 0.9705 0.5150 0.7284 0.8493 0.1807 0.9988 0.4923 0.7746 0.9733 0.7229 0.9456 0.2459 0.1212 0.9899 0.3242 0.0989 0.2780 0.3512 0.2708 0.5926 0.0715 0.2271 0.5188 0.1771 0.9741 0.1885 0.5859 0.5517 0.9505 0.2560
GSEA 0.0000 0.0000 0.0000 0.0000 0.0025 0.0044 0.0045 0.0000 0.0070 0.0221 0.0000 0.0022 0.0000 0.0261 0.0217 0.0132 0.0412 0.0025 0.0195 0.0452 0.0217 0.0115 0.0235 0.0345 0.0352 0.0390 0.0141 0.0113 0.0398 0.0246 0.0250 0.0119 0.0118 0.026 0.0438 0.0374 0.0041 0.0279 0.0167 0.0392 0.0383 0.0348 0.0466 0.0312 0.0237 0.0321 0.0023 0.0304 0.0317 0.0343 0.0234 0.0350 0.0465 0.0498 0.0363 0.0435 0.0448 0.0260 0.0149 0.0359 0.0499 0.0325 0.0493 0.0209 0.0254 0.0238 0.0477 0.0303 0.0333 0.0406 0.0301 0.0424 0.0464 0.0448 0.0334 0.0000 0.0018 0.0084 0.0172 0.0038 0.0019 0.0134 0.0122 0.0247 0.0018 0.0274 0.0179 0.0164 0.0281 0.0263 0.0232 0.0229 0.0272 0.0234 0.0111 0.0348 0.0469 0.0281 0.0218 0.0216 0.0325 0.0237 0.0423 0.0447 0.0324 0.0144 0.0268 0.0414 0.0318 0.0417 0.0446 0.0323 0.0460 0.0480 0.0364 0.0466 0.0244 0.0456 0.0454 0.0348 0.0479 0.0199 0.0263 0.0275 0.0447 0.0473 0.0422 0.0377 0.0412

Close cluster

# stopCluster(cl)

PCA plot of pathways deemed significant in MPEA but not GSEA

library(ggfortify)
## Loading required package: ggplot2
for (name in (sort(Significant_in_dcor_not_in_GSEA, decreasing = F))){
strongestpathwaydcor <- unname(unlist(pathway_collapsed[name]))
expressions_pathway <- as.data.frame(expressions[,which(colnames(expressions)%in% strongestpathwaydcor)])
genotypes_category <- ifelse(genotypes==1, "MUT", "WT")
genotypes_category <- as.data.frame(genotypes_category)
print(name)
print(autoplot(prcomp(expressions_pathway), data = genotypes_category, colour='genotypes_category' )+theme_bw()) 

# pcoa.obj <- pcoa(D = dist(expressions_pathway), correction="none", rn=NULL)
# biplot.pcoa(pcoa.obj)
}
## [1] "ACEVEDO_FGFR1_TARGETS_IN_PROSTATE_CANCER_MODEL_UP"

## [1] "AGUIRRE_PANCREATIC_CANCER_COPY_NUMBER_DN"

## [1] "ALONSO_METASTASIS_NEURAL_UP"

## [1] "AMIT_EGF_RESPONSE_120_HELA"

## [1] "AMIT_EGF_RESPONSE_120_MCF10A"

## [1] "APPIERTO_RESPONSE_TO_FENRETINIDE_UP"

## [1] "BARRIER_CANCER_RELAPSE_NORMAL_SAMPLE_UP"

## [1] "BASAKI_YBX1_TARGETS_DN"

## [1] "BENPORATH_CYCLING_GENES"

## [1] "BHAT_ESR1_TARGETS_VIA_AKT1_UP"

## [1] "BILD_HRAS_ONCOGENIC_SIGNATURE"

## [1] "BIOCARTA_ACTINY_PATHWAY"

## [1] "BIOCARTA_ATM_PATHWAY"

## [1] "BIOCARTA_BAD_PATHWAY"

## [1] "BIOCARTA_CALCINEURIN_PATHWAY"

## [1] "BIOCARTA_CERAMIDE_PATHWAY"

## [1] "BIOCARTA_FAS_PATHWAY"

## [1] "BIOCARTA_HIVNEF_PATHWAY"

## [1] "BIOCARTA_KERATINOCYTE_PATHWAY"

## [1] "BIOCARTA_MITOCHONDRIA_PATHWAY"

## [1] "BIOCARTA_MYOSIN_PATHWAY"

## [1] "BIOCARTA_RAC1_PATHWAY"

## [1] "BOYAULT_LIVER_CANCER_SUBCLASS_G1_UP"

## [1] "BOYAULT_LIVER_CANCER_SUBCLASS_G123_DN"

## [1] "BOYLAN_MULTIPLE_MYELOMA_C_CLUSTER_UP"

## [1] "BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_UP"

## [1] "CAFFAREL_RESPONSE_TO_THC_24HR_5_UP"

## [1] "CHEOK_RESPONSE_TO_MERCAPTOPURINE_DN"

## [1] "CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_CDC25_DN"

## [1] "CHIARETTI_ACUTE_LYMPHOBLASTIC_LEUKEMIA_ZAP70"

## [1] "CHUANG_OXIDATIVE_STRESS_RESPONSE_UP"

## [1] "COATES_MACROPHAGE_M1_VS_M2_DN"

## [1] "COATES_MACROPHAGE_M1_VS_M2_UP"

## [1] "CONCANNON_APOPTOSIS_BY_EPOXOMICIN_UP"

## [1] "CORRE_MULTIPLE_MYELOMA_UP"

## [1] "CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_3"

## [1] "CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5"

## [1] "DARWICHE_SKIN_TUMOR_PROMOTER_DN"

## [1] "DOANE_BREAST_CANCER_ESR1_UP"

## [1] "DURAND_STROMA_NS_UP"

## [1] "DUTTA_APOPTOSIS_VIA_NFKB"

## [1] "ELVIDGE_HYPOXIA_BY_DMOG_UP"

## [1] "ELVIDGE_HYPOXIA_UP"

## [1] "FARMER_BREAST_CANCER_BASAL_VS_LULMINAL"

## [1] "FERNANDEZ_BOUND_BY_MYC"

## [1] "FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_OK_VS_DONOR_DN"

## [1] "GALINDO_IMMUNE_RESPONSE_TO_ENTEROTOXIN"

## [1] "GALLUZZI_PREVENT_MITOCHONDIAL_PERMEABILIZATION"

## [1] "GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_TURQUOISE_UP"

## [1] "GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_UP"

## [1] "GAZDA_DIAMOND_BLACKFAN_ANEMIA_MYELOID_UP"

## [1] "GHANDHI_DIRECT_IRRADIATION_UP"

## [1] "GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_UP"

## [1] "GOLUB_ALL_VS_AML_DN"

## [1] "GOZGIT_ESR1_TARGETS_DN"

## [1] "GRADE_COLON_AND_RECTAL_CANCER_DN"

## [1] "GRADE_COLON_AND_RECTAL_CANCER_UP"

## [1] "GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP"

## [1] "GRAHAM_CML_QUIESCENT_VS_NORMAL_QUIESCENT_DN"

## [1] "GROSS_HIF1A_TARGETS_DN"

## [1] "GYORFFY_DOXORUBICIN_RESISTANCE"

## [1] "HAMAI_APOPTOSIS_VIA_TRAIL_DN"

## [1] "HASLINGER_B_CLL_WITH_MUTATED_VH_GENES"

## [1] "HELLER_HDAC_TARGETS_DN"

## [1] "HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_DN"

## [1] "HELLER_SILENCED_BY_METHYLATION_DN"

## [1] "HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_4NM_UP"

## [1] "HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_1_DN"

## [1] "HOEBEKE_LYMPHOID_STEM_CELL_DN"

## [1] "HOELZEL_NF1_TARGETS_UP"

## [1] "HOFFMANN_IMMATURE_TO_MATURE_B_LYMPHOCYTE_UP"

## [1] "HOFFMANN_PRE_BI_TO_LARGE_PRE_BII_LYMPHOCYTE_UP"

## [1] "HOFMANN_MYELODYSPLASTIC_SYNDROM_LOW_RISK_UP"

## [1] "HOFMANN_MYELODYSPLASTIC_SYNDROM_RISK_UP"

## [1] "IIZUKA_LIVER_CANCER_PROGRESSION_L0_L1_DN"

## [1] "JI_METASTASIS_REPRESSED_BY_STK11"

## [1] "KAN_RESPONSE_TO_ARSENIC_TRIOXIDE"

## [1] "KANG_IMMORTALIZED_BY_TERT_UP"

## [1] "KASLER_HDAC7_TARGETS_1_UP"

## [1] "KATSANOU_ELAVL1_TARGETS_UP"

## [1] "KAUFFMANN_DNA_REPLICATION_GENES"

## [1] "KEGG_AMYOTROPHIC_LATERAL_SCLEROSIS_ALS"

## [1] "KEGG_APOPTOSIS"

## [1] "KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION"

## [1] "KEGG_EPITHELIAL_CELL_SIGNALING_IN_HELICOBACTER_PYLORI_INFECTION"

## [1] "KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS"

## [1] "KEGG_INOSITOL_PHOSPHATE_METABOLISM"

## [1] "KEGG_NOD_LIKE_RECEPTOR_SIGNALING_PATHWAY"

## [1] "KEGG_NOTCH_SIGNALING_PATHWAY"

## [1] "KEGG_OOCYTE_MEIOSIS"

## [1] "KEGG_PRION_DISEASES"

## [1] "KIM_LIVER_CANCER_POOR_SURVIVAL_DN"

## [1] "KIM_MYCN_AMPLIFICATION_TARGETS_UP"

## [1] "KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP"

## [1] "KIM_WT1_TARGETS_12HR_UP"

## [1] "KOKKINAKIS_METHIONINE_DEPRIVATION_96HR_DN"

## [1] "KRIEG_HYPOXIA_VIA_KDM3A"

## [1] "KRIEG_KDM3A_TARGETS_NOT_HYPOXIA"

## [1] "KYNG_RESPONSE_TO_H2O2"

## [1] "LABBE_WNT3A_TARGETS_DN"

## [1] "LANDIS_ERBB2_BREAST_TUMORS_65_UP"

## [1] "LAU_APOPTOSIS_CDKN2A_UP"

## [1] "LEE_LIVER_CANCER_SURVIVAL_UP"

## [1] "LEE_NEURAL_CREST_STEM_CELL_DN"

## [1] "LENAOUR_DENDRITIC_CELL_MATURATION_UP"

## [1] "LIU_PROSTATE_CANCER_UP"

## [1] "LIU_SMARCA4_TARGETS"

## [1] "MAGRANGEAS_MULTIPLE_MYELOMA_IGLL_VS_IGLK_UP"

## [1] "MAHADEVAN_RESPONSE_TO_MP470_DN"

## [1] "MARCHINI_TRABECTEDIN_RESISTANCE_DN"

## [1] "MARKS_HDAC_TARGETS_UP"

## [1] "MARZEC_IL2_SIGNALING_DN"

## [1] "MEISSNER_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3"

## [1] "MENSSEN_MYC_TARGETS"

## [1] "MIKKELSEN_ES_ICP_WITH_H3K27ME3"

## [1] "MIKKELSEN_ES_ICP_WITH_H3K4ME3"

## [1] "MIKKELSEN_IPS_ICP_WITH_H3K27ME3"

## [1] "MIKKELSEN_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3"

## [1] "MOHANKUMAR_HOXA1_TARGETS_DN"

## [1] "MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_UP"

## [1] "MOOTHA_GLUCONEOGENESIS"

## [1] "MOOTHA_HUMAN_MITODB_6_2002"

## [1] "MOOTHA_PGC"

## [1] "MORI_SMALL_PRE_BII_LYMPHOCYTE_DN"

## [1] "MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_UP"

## [1] "MULLIGHAN_NPM1_SIGNATURE_3_UP"

## [1] "NAGASHIMA_NRG1_SIGNALING_UP"

## [1] "NAKAJIMA_MAST_CELL"

## [1] "NAKAMURA_ADIPOGENESIS_LATE_DN"

## [1] "OHGUCHI_LIVER_HNF4A_TARGETS_UP"

## [1] "ONDER_CDH1_TARGETS_1_UP"

## [1] "OUILLETTE_CLL_13Q14_DELETION_UP"

## [1] "PACHER_TARGETS_OF_IGF1_AND_IGF2_UP"

## [1] "PID_BMP_PATHWAY"

## [1] "PID_CDC42_PATHWAY"

## [1] "PID_E2F_PATHWAY"

## [1] "PID_FAS_PATHWAY"

## [1] "PID_HIV_NEF_PATHWAY"

## [1] "PID_RAC1_PATHWAY"

## [1] "PID_RHODOPSIN_PATHWAY"

## [1] "PLASARI_TGFB1_SIGNALING_VIA_NFIC_10HR_UP"

## [1] "POOLA_INVASIVE_BREAST_CANCER_UP"

## [1] "PRAMOONJAGO_SOX4_TARGETS_UP"

## [1] "PROVENZANI_METASTASIS_DN"

## [1] "PROVENZANI_METASTASIS_UP"

## [1] "PURBEY_TARGETS_OF_CTBP1_NOT_SATB1_UP"

## [1] "REACTOME_CDK_MEDIATED_PHOSPHORYLATION_AND_REMOVAL_OF_CDC6"

## [1] "REACTOME_CELL_CYCLE_CHECKPOINTS"

## [1] "REACTOME_CYCLIN_E_ASSOCIATED_EVENTS_DURING_G1_S_TRANSITION_"

## [1] "REACTOME_DNA_REPLICATION"

## [1] "REACTOME_DOWNSTREAM_SIGNAL_TRANSDUCTION"

## [1] "REACTOME_FORMATION_OF_INCISION_COMPLEX_IN_GG_NER"

## [1] "REACTOME_G0_AND_EARLY_G1"

## [1] "REACTOME_G1_S_TRANSITION"

## [1] "REACTOME_GLUCONEOGENESIS"

## [1] "REACTOME_INTRINSIC_PATHWAY_FOR_APOPTOSIS"

## [1] "REACTOME_M_G1_TRANSITION"

## [1] "REACTOME_METABOLISM_OF_NUCLEOTIDES"

## [1] "REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS"

## [1] "REACTOME_MITOTIC_G2_G2_M_PHASES"

## [1] "REACTOME_MITOTIC_M_M_G1_PHASES"

## [1] "REACTOME_ORC1_REMOVAL_FROM_CHROMATIN"

## [1] "REACTOME_P53_DEPENDENT_G1_DNA_DAMAGE_RESPONSE"

## [1] "REACTOME_PI_3K_CASCADE"

## [1] "REACTOME_PI_METABOLISM"

## [1] "REACTOME_PI3K_EVENTS_IN_ERBB2_SIGNALING"

## [1] "REACTOME_PI3K_EVENTS_IN_ERBB4_SIGNALING"

## [1] "REACTOME_POTASSIUM_CHANNELS"

## [1] "REACTOME_REGULATION_OF_MITOTIC_CELL_CYCLE"

## [1] "REACTOME_SCFSKP2_MEDIATED_DEGRADATION_OF_P27_P21"

## [1] "REACTOME_SIGNALING_BY_SCF_KIT"

## [1] "REACTOME_SYNTHESIS_OF_DNA"

## [1] "REACTOME_VOLTAGE_GATED_POTASSIUM_CHANNELS"

## [1] "RIGGI_EWING_SARCOMA_PROGENITOR_UP"

## [1] "ROSS_AML_OF_FAB_M7_TYPE"

## [1] "RUIZ_TNC_TARGETS_UP"

## [1] "SA_CASPASE_CASCADE"

## [1] "SAGIV_CD24_TARGETS_DN"

## [1] "SAKAI_TUMOR_INFILTRATING_MONOCYTES_DN"

## [1] "SATO_SILENCED_BY_DEACETYLATION_IN_PANCREATIC_CANCER"

## [1] "SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_DN"

## [1] "SEITZ_NEOPLASTIC_TRANSFORMATION_BY_8P_DELETION_DN"

## [1] "SEKI_INFLAMMATORY_RESPONSE_LPS_UP"

## [1] "SENGUPTA_NASOPHARYNGEAL_CARCINOMA_WITH_LMP1_UP"

## [1] "SESTO_RESPONSE_TO_UV_C0"

## [1] "SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM6"

## [1] "SHIN_B_CELL_LYMPHOMA_CLUSTER_7"

## [1] "SHIN_B_CELL_LYMPHOMA_CLUSTER_8"

## [1] "SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_UP"

## [1] "SMID_BREAST_CANCER_LUMINAL_B_UP"

## [1] "SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_UP"

## [1] "SPIRA_SMOKERS_LUNG_CANCER_UP"

## [1] "STEIN_ESRRA_TARGETS"

## [1] "STEIN_ESRRA_TARGETS_UP"

## [1] "TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_8D_UP"

## [1] "TENEDINI_MEGAKARYOCYTE_MARKERS"

## [1] "TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_HSC_UP"

## [1] "TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_UP"

## [1] "TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINDED_IN_ERYTHROCYTE_UP"

## [1] "TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINED_IN_MONOCYTE_UP"

## [1] "TSAI_RESPONSE_TO_IONIZING_RADIATION"

## [1] "VALK_AML_CLUSTER_16"

## [1] "VALK_AML_CLUSTER_3"

## [1] "VALK_AML_CLUSTER_7"

## [1] "VARELA_ZMPSTE24_TARGETS_UP"

## [1] "VECCHI_GASTRIC_CANCER_EARLY_UP"

## [1] "VERHAAK_AML_WITH_NPM1_MUTATED_UP"

## [1] "VIETOR_IFRD1_TARGETS"

## [1] "WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_8D"

## [1] "WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_WITH_H4K20ME1_MARK"

## [1] "WALLACE_PROSTATE_CANCER_UP"

## [1] "WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_UP"

## [1] "WANG_CLIM2_TARGETS_DN"

## [1] "WANG_ESOPHAGUS_CANCER_VS_NORMAL_DN"

## [1] "WANG_METHYLATED_IN_BREAST_CANCER"

## [1] "WANG_SMARCE1_TARGETS_DN"

## [1] "WANG_TNF_TARGETS"

## [1] "WHITFIELD_CELL_CYCLE_LITERATURE"

## [1] "WHITFIELD_CELL_CYCLE_M_G1"

## [1] "WINZEN_DEGRADED_VIA_KHSRP"

## [1] "WU_HBX_TARGETS_1_UP"

## [1] "WU_HBX_TARGETS_2_UP"

## [1] "YAMAZAKI_TCEB3_TARGETS_DN"

## [1] "ZHANG_PROLIFERATING_VS_QUIESCENT"

PCA plot of pathways deemed significant in GSEA but not MPEA

rownames(gsea_results_significant)
##   [1] "AMUNDSON_DNA_DAMAGE_RESPONSE_TP53"                           
##   [2] "WARTERS_IR_RESPONSE_5GY"                                     
##   [3] "MANN_RESPONSE_TO_AMIFOSTINE_UP"                              
##   [4] "WARTERS_RESPONSE_TO_IR_SKIN"                                 
##   [5] "QUINTENS_EMBRYONIC_BRAIN_RESPONSE_TO_IR"                     
##   [6] "BIOCARTA_P53_PATHWAY"                                        
##   [7] "MACAEVA_PBMC_RESPONSE_TO_IR"                                 
##   [8] "WILENSKY_RESPONSE_TO_DARAPLADIB"                             
##   [9] "LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN"                      
##  [10] "REACTOME_AMINE_LIGAND_BINDING_RECEPTORS"                     
##  [11] "PID_TAP63_PATHWAY"                                           
##  [12] "REACTOME_PEPTIDE_LIGAND_BINDING_RECEPTORS"                   
##  [13] "BIOCARTA_P53HYPOXIA_PATHWAY"                                 
##  [14] "LIAN_LIPA_TARGETS_3M"                                        
##  [15] "REACTOME_PHASE_II_CONJUGATION"                               
##  [16] "KERLEY_RESPONSE_TO_CISPLATIN_UP"                             
##  [17] "ODONNELL_METASTASIS_UP"                                      
##  [18] "VILIMAS_NOTCH1_TARGETS_DN"                                   
##  [19] "REACTOME_CLASS_A1_RHODOPSIN_LIKE_RECEPTORS"                  
##  [20] "NIKOLSKY_BREAST_CANCER_16Q24_AMPLICON"                       
##  [21] "MEISSNER_NPC_HCP_WITH_H3K4ME2_AND_H3K27ME3"                  
##  [22] "PID_P53_DOWNSTREAM_PATHWAY"                                  
##  [23] "PID_P73PATHWAY"                                              
##  [24] "GENTILE_UV_LOW_DOSE_UP"                                      
##  [25] "LIAN_LIPA_TARGETS_6M"                                        
##  [26] "NIELSEN_GIST_AND_SYNOVIAL_SARCOMA_DN"                        
##  [27] "REACTOME_EFFECTS_OF_PIP2_HYDROLYSIS"                         
##  [28] "REACTOME_LIPOPROTEIN_METABOLISM"                             
##  [29] "FISCHER_DIRECT_P53_TARGETS_META_ANALYSIS"                    
##  [30] "VALK_AML_CLUSTER_13"                                         
##  [31] "KEGG_P53_SIGNALING_PATHWAY"                                  
##  [32] "BIOCARTA_CYTOKINE_PATHWAY"                                   
##  [33] "BIOCARTA_CK1_PATHWAY"                                        
##  [34] "KEGG_CALCIUM_SIGNALING_PATHWAY"                              
##  [35] "VANDESLUIS_COMMD1_TARGETS_GROUP_4_UP"                        
##  [36] "REACTOME_CA_DEPENDENT_EVENTS"                                
##  [37] "ROYLANCE_BREAST_CANCER_16Q_COPY_NUMBER_UP"                   
##  [38] "CHEN_ETV5_TARGETS_SERTOLI"                                   
##  [39] "ONGUSAHA_TP53_TARGETS"                                       
##  [40] "TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_DN"           
##  [41] "REACTOME_REGULATION_OF_IFNA_SIGNALING"                       
##  [42] "BIOCARTA_NO2IL12_PATHWAY"                                    
##  [43] "SU_PANCREAS"                                                 
##  [44] "BIOCARTA_INFLAM_PATHWAY"                                     
##  [45] "REACTOME_CHEMOKINE_RECEPTORS_BIND_CHEMOKINES"                
##  [46] "HASLINGER_B_CLL_WITH_CHROMOSOME_12_TRISOMY"                  
##  [47] "REACTOME_G_ALPHA_I_SIGNALLING_EVENTS"                        
##  [48] "REACTOME_PLC_BETA_MEDIATED_EVENTS"                           
##  [49] "MATZUK_SPERMATOGONIA"                                        
##  [50] "REACTOME_GPCR_LIGAND_BINDING"                                
##  [51] "REACTOME_DAG_AND_IP3_SIGNALING"                              
##  [52] "CEBALLOS_TARGETS_OF_TP53_AND_MYC_DN"                         
##  [53] "YAUCH_HEDGEHOG_SIGNALING_PARACRINE_DN"                       
##  [54] "PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_DN"                   
##  [55] "KEGG_OLFACTORY_TRANSDUCTION"                                 
##  [56] "MIKKELSEN_MCV6_ICP_WITH_H3K27ME3"                            
##  [57] "KANNAN_TP53_TARGETS_UP"                                      
##  [58] "EBAUER_TARGETS_OF_PAX3_FOXO1_FUSION_DN"                      
##  [59] "PID_NCADHERIN_PATHWAY"                                       
##  [60] "FIGUEROA_AML_METHYLATION_CLUSTER_5_DN"                       
##  [61] "CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_UP"                      
##  [62] "REACTOME_G_ALPHA_Q_SIGNALLING_EVENTS"                        
##  [63] "BREDEMEYER_RAG_SIGNALING_VIA_ATM_NOT_VIA_NFKB_UP"            
##  [64] "THEODOROU_MAMMARY_TUMORIGENESIS"                             
##  [65] "HOLLEMAN_VINCRISTINE_RESISTANCE_ALL_UP"                      
##  [66] "NIELSEN_SYNOVIAL_SARCOMA_DN"                                 
##  [67] "MCMURRAY_TP53_HRAS_COOPERATION_RESPONSE_DN"                  
##  [68] "REACTOME_PIP3_ACTIVATES_AKT_SIGNALING"                       
##  [69] "ABE_VEGFA_TARGETS_2HR"                                       
##  [70] "REACTOME_NITRIC_OXIDE_STIMULATES_GUANYLATE_CYCLASE"          
##  [71] "REACTOME_PHOSPHOLIPASE_C_MEDIATED_CASCADE"                   
##  [72] "MARSON_FOXP3_TARGETS_DN"                                     
##  [73] "REACTOME_GPCR_DOWNSTREAM_SIGNALING"                          
##  [74] "GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLACK_UP"      
##  [75] "RAMALHO_STEMNESS_DN"                                         
##  [76] "REACTOME_LYSOSOME_VESICLE_BIOGENESIS"                        
##  [77] "FOSTER_KDM1A_TARGETS_UP"                                     
##  [78] "KAMMINGA_SENESCENCE"                                         
##  [79] "ODONNELL_TFRC_TARGETS_UP"                                    
##  [80] "GAVIN_FOXP3_TARGETS_CLUSTER_T4"                              
##  [81] "DARWICHE_PAPILLOMA_PROGRESSION_RISK"                         
##  [82] "YAMASHITA_LIVER_CANCER_STEM_CELL_DN"                         
##  [83] "PEDRIOLI_MIR31_TARGETS_DN"                                   
##  [84] "BENPORATH_PRC2_TARGETS"                                      
##  [85] "HESS_TARGETS_OF_HOXA9_AND_MEIS1_DN"                          
##  [86] "SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A12"                       
##  [87] "SMIRNOV_RESPONSE_TO_IR_2HR_UP"                               
##  [88] "OHGUCHI_LIVER_HNF4A_TARGETS_DN"                              
##  [89] "MA_MYELOID_DIFFERENTIATION_DN"                               
##  [90] "ICHIBA_GRAFT_VERSUS_HOST_DISEASE_35D_DN"                     
##  [91] "SMIRNOV_RESPONSE_TO_IR_6HR_UP"                               
##  [92] "LABBE_TGFB1_TARGETS_DN"                                      
##  [93] "REACTOME_SIGNALING_BY_GPCR"                                  
##  [94] "MCLACHLAN_DENTAL_CARIES_UP"                                  
##  [95] "BIOCARTA_CHEMICAL_PATHWAY"                                   
##  [96] "PID_INTEGRIN_CS_PATHWAY"                                     
##  [97] "REACTOME_GAB1_SIGNALOSOME"                                   
##  [98] "FLORIO_NEOCORTEX_BASAL_RADIAL_GLIA_UP"                       
##  [99] "NABA_SECRETED_FACTORS"                                       
## [100] "BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_TRANS"        
## [101] "XU_HGF_TARGETS_REPRESSED_BY_AKT1_DN"                         
## [102] "ONO_FOXP3_TARGETS_DN"                                        
## [103] "KEGG_TYPE_I_DIABETES_MELLITUS"                               
## [104] "HOQUE_METHYLATED_IN_CANCER"                                  
## [105] "ZHANG_GATA6_TARGETS_DN"                                      
## [106] "KONDO_PROSTATE_CANCER_WITH_H3K27ME3"                         
## [107] "PID_IL4_2PATHWAY"                                            
## [108] "MIKKELSEN_NPC_HCP_WITH_H3K27ME3"                             
## [109] "REN_ALVEOLAR_RHABDOMYOSARCOMA_UP"                            
## [110] "RIZKI_TUMOR_INVASIVENESS_3D_UP"                              
## [111] "TAYLOR_METHYLATED_IN_ACUTE_LYMPHOBLASTIC_LEUKEMIA"           
## [112] "BROWNE_HCMV_INFECTION_2HR_DN"                                
## [113] "ANDERSEN_CHOLANGIOCARCINOMA_CLASS2"                          
## [114] "REACTOME_ASPARAGINE_N_LINKED_GLYCOSYLATION"                  
## [115] "MORI_PLASMA_CELL_UP"                                         
## [116] "WANG_RESPONSE_TO_BEXAROTENE_DN"                              
## [117] "FAELT_B_CLL_WITH_VH3_21_DN"                                  
## [118] "TSENG_ADIPOGENIC_POTENTIAL_UP"                               
## [119] "KEGG_N_GLYCAN_BIOSYNTHESIS"                                  
## [120] "WELCSH_BRCA1_TARGETS_UP"                                     
## [121] "PID_WNT_NONCANONICAL_PATHWAY"                                
## [122] "HINATA_NFKB_TARGETS_KERATINOCYTE_DN"                         
## [123] "REACTOME_GRB2_EVENTS_IN_ERBB2_SIGNALING"                     
## [124] "BIOCARTA_RAS_PATHWAY"                                        
## [125] "RODRIGUES_NTN1_TARGETS_DN"                                   
## [126] "PID_EPHB_FWD_PATHWAY"                                        
## [127] "BURTON_ADIPOGENESIS_11"                                      
## [128] "REACTOME_NOTCH1_INTRACELLULAR_DOMAIN_REGULATES_TRANSCRIPTION"
## [129] "REACTOME_PEROXISOMAL_LIPID_METABOLISM"                       
## [130] "NUYTTEN_NIPP1_TARGETS_DN"                                    
## [131] "BENPORATH_ES_CORE_NINE_CORRELATED"                           
## [132] "JI_RESPONSE_TO_FSH_DN"                                       
## [133] "DORSAM_HOXA9_TARGETS_UP"                                     
## [134] "PID_HDAC_CLASSI_PATHWAY"                                     
## [135] "BIOCARTA_IGF1_PATHWAY"                                       
## [136] "REACTOME_PROLONGED_ERK_ACTIVATION_EVENTS"                    
## [137] "PID_HDAC_CLASSII_PATHWAY"                                    
## [138] "AMIT_SERUM_RESPONSE_120_MCF10A"                              
## [139] "WINTER_HYPOXIA_UP"                                           
## [140] "DACOSTA_UV_RESPONSE_VIA_ERCC3_TTD_DN"                        
## [141] "BARIS_THYROID_CANCER_DN"                                     
## [142] "LANDIS_ERBB2_BREAST_TUMORS_324_UP"                           
## [143] "SEIDEN_MET_SIGNALING"                                        
## [144] "TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_DUCTAL_NORMAL_DN"     
## [145] "REACTOME_SHC1_EVENTS_IN_ERBB4_SIGNALING"                     
## [146] "LEE_AGING_MUSCLE_DN"                                         
## [147] "BIOCARTA_FMLP_PATHWAY"                                       
## [148] "BIOCARTA_NGF_PATHWAY"                                        
## [149] "REACTOME_ENOS_ACTIVATION_AND_REGULATION"                     
## [150] "GROSS_HYPOXIA_VIA_HIF1A_DN"                                  
## [151] "STONER_ESOPHAGEAL_CARCINOGENESIS_UP"                         
## [152] "BIOCARTA_BCR_PATHWAY"                                        
## [153] "PID_AVB3_OPN_PATHWAY"                                        
## [154] "SA_B_CELL_RECEPTOR_COMPLEXES"                                
## [155] "PUIFFE_INVASION_INHIBITED_BY_ASCITES_UP"                     
## [156] "TRACEY_RESISTANCE_TO_IFNA2_DN"                               
## [157] "KAAB_FAILED_HEART_ATRIUM_DN"                                 
## [158] "WANG_TUMOR_INVASIVENESS_DN"                                  
## [159] "FORTSCHEGGER_PHF8_TARGETS_DN"                                
## [160] "SESTO_RESPONSE_TO_UV_C7"                                     
## [161] "WANG_HCP_PROSTATE_CANCER"                                    
## [162] "REACTOME_CTLA4_INHIBITORY_SIGNALING"                         
## [163] "KYNG_DNA_DAMAGE_BY_GAMMA_AND_UV_RADIATION"                   
## [164] "GOTZMANN_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_DN"
for (name in (Significant_in_GSEA_not_in_dcor)){
  strongestpathwaydcor <- unname(unlist(pathway_collapsed[name]))
  expressions_pathway <- as.data.frame(expressions[,which(colnames(expressions)%in% strongestpathwaydcor)])
  genotypes_category <- ifelse(genotypes==1, "MUT", "WT")
  genotypes_category <- as.data.frame(genotypes_category)
  print(name)
  print(autoplot(prcomp(expressions_pathway), data = genotypes_category, colour='genotypes_category' )+theme_bw()+ggtitle(label = "name")) 
  
  # pcoa.obj <- pcoa(D = dist(expressions_pathway), correction="none", rn=NULL)
  # biplot.pcoa(pcoa.obj)
}
## [1] "AMUNDSON_DNA_DAMAGE_RESPONSE_TP53"

## [1] "BIOCARTA_P53_PATHWAY"

## [1] "WILENSKY_RESPONSE_TO_DARAPLADIB"

## [1] "LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN"

## [1] "REACTOME_PEPTIDE_LIGAND_BINDING_RECEPTORS"

## [1] "BIOCARTA_P53HYPOXIA_PATHWAY"

## [1] "REACTOME_PHASE_II_CONJUGATION"

## [1] "ODONNELL_METASTASIS_UP"

## [1] "REACTOME_CLASS_A1_RHODOPSIN_LIKE_RECEPTORS"

## [1] "NIKOLSKY_BREAST_CANCER_16Q24_AMPLICON"

## [1] "MEISSNER_NPC_HCP_WITH_H3K4ME2_AND_H3K27ME3"

## [1] "NIELSEN_GIST_AND_SYNOVIAL_SARCOMA_DN"

## [1] "REACTOME_EFFECTS_OF_PIP2_HYDROLYSIS"

## [1] "REACTOME_LIPOPROTEIN_METABOLISM"

## [1] "VALK_AML_CLUSTER_13"

## [1] "KEGG_P53_SIGNALING_PATHWAY"

## [1] "BIOCARTA_CYTOKINE_PATHWAY"

## [1] "KEGG_CALCIUM_SIGNALING_PATHWAY"

## [1] "VANDESLUIS_COMMD1_TARGETS_GROUP_4_UP"

## [1] "REACTOME_CA_DEPENDENT_EVENTS"

## [1] "CHEN_ETV5_TARGETS_SERTOLI"

## [1] "ONGUSAHA_TP53_TARGETS"

## [1] "TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_DN"

## [1] "REACTOME_REGULATION_OF_IFNA_SIGNALING"

## [1] "BIOCARTA_NO2IL12_PATHWAY"

## [1] "BIOCARTA_INFLAM_PATHWAY"

## [1] "REACTOME_CHEMOKINE_RECEPTORS_BIND_CHEMOKINES"

## [1] "REACTOME_G_ALPHA_I_SIGNALLING_EVENTS"

## [1] "REACTOME_PLC_BETA_MEDIATED_EVENTS"

## [1] "REACTOME_GPCR_LIGAND_BINDING"

## [1] "REACTOME_DAG_AND_IP3_SIGNALING"

## [1] "CEBALLOS_TARGETS_OF_TP53_AND_MYC_DN"

## [1] "YAUCH_HEDGEHOG_SIGNALING_PARACRINE_DN"

## [1] "PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_DN"

## [1] "KEGG_OLFACTORY_TRANSDUCTION"

## [1] "MIKKELSEN_MCV6_ICP_WITH_H3K27ME3"

## [1] "PID_NCADHERIN_PATHWAY"

## [1] "FIGUEROA_AML_METHYLATION_CLUSTER_5_DN"

## [1] "REACTOME_G_ALPHA_Q_SIGNALLING_EVENTS"

## [1] "BREDEMEYER_RAG_SIGNALING_VIA_ATM_NOT_VIA_NFKB_UP"

## [1] "THEODOROU_MAMMARY_TUMORIGENESIS"

## [1] "HOLLEMAN_VINCRISTINE_RESISTANCE_ALL_UP"

## [1] "NIELSEN_SYNOVIAL_SARCOMA_DN"

## [1] "REACTOME_NITRIC_OXIDE_STIMULATES_GUANYLATE_CYCLASE"

## [1] "REACTOME_PHOSPHOLIPASE_C_MEDIATED_CASCADE"

## [1] "MARSON_FOXP3_TARGETS_DN"

## [1] "REACTOME_GPCR_DOWNSTREAM_SIGNALING"

## [1] "GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLACK_UP"

## [1] "REACTOME_LYSOSOME_VESICLE_BIOGENESIS"

## [1] "KAMMINGA_SENESCENCE"

## [1] "ODONNELL_TFRC_TARGETS_UP"

## [1] "GAVIN_FOXP3_TARGETS_CLUSTER_T4"

## [1] "DARWICHE_PAPILLOMA_PROGRESSION_RISK"

## [1] "YAMASHITA_LIVER_CANCER_STEM_CELL_DN"

## [1] "PEDRIOLI_MIR31_TARGETS_DN"

## [1] "BENPORATH_PRC2_TARGETS"

## [1] "HESS_TARGETS_OF_HOXA9_AND_MEIS1_DN"

## [1] "SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A12"

## [1] "OHGUCHI_LIVER_HNF4A_TARGETS_DN"

## [1] "MA_MYELOID_DIFFERENTIATION_DN"

## [1] "ICHIBA_GRAFT_VERSUS_HOST_DISEASE_35D_DN"

## [1] "REACTOME_SIGNALING_BY_GPCR"

## [1] "PID_INTEGRIN_CS_PATHWAY"

## [1] "FLORIO_NEOCORTEX_BASAL_RADIAL_GLIA_UP"

## [1] "BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_TRANS"

## [1] "XU_HGF_TARGETS_REPRESSED_BY_AKT1_DN"

## [1] "ONO_FOXP3_TARGETS_DN"

## [1] "KEGG_TYPE_I_DIABETES_MELLITUS"

## [1] "HOQUE_METHYLATED_IN_CANCER"

## [1] "ZHANG_GATA6_TARGETS_DN"

## [1] "KONDO_PROSTATE_CANCER_WITH_H3K27ME3"

## [1] "PID_IL4_2PATHWAY"

## [1] "MIKKELSEN_NPC_HCP_WITH_H3K27ME3"

## [1] "REN_ALVEOLAR_RHABDOMYOSARCOMA_UP"

## [1] "RIZKI_TUMOR_INVASIVENESS_3D_UP"

## [1] "TAYLOR_METHYLATED_IN_ACUTE_LYMPHOBLASTIC_LEUKEMIA"

## [1] "BROWNE_HCMV_INFECTION_2HR_DN"

## [1] "ANDERSEN_CHOLANGIOCARCINOMA_CLASS2"

## [1] "REACTOME_ASPARAGINE_N_LINKED_GLYCOSYLATION"

## [1] "MORI_PLASMA_CELL_UP"

## [1] "WANG_RESPONSE_TO_BEXAROTENE_DN"

## [1] "FAELT_B_CLL_WITH_VH3_21_DN"

## [1] "TSENG_ADIPOGENIC_POTENTIAL_UP"

## [1] "KEGG_N_GLYCAN_BIOSYNTHESIS"

## [1] "WELCSH_BRCA1_TARGETS_UP"

## [1] "PID_WNT_NONCANONICAL_PATHWAY"

## [1] "HINATA_NFKB_TARGETS_KERATINOCYTE_DN"

## [1] "REACTOME_GRB2_EVENTS_IN_ERBB2_SIGNALING"

## [1] "BIOCARTA_RAS_PATHWAY"

## [1] "RODRIGUES_NTN1_TARGETS_DN"

## [1] "PID_EPHB_FWD_PATHWAY"

## [1] "BURTON_ADIPOGENESIS_11"

## [1] "REACTOME_NOTCH1_INTRACELLULAR_DOMAIN_REGULATES_TRANSCRIPTION"

## [1] "REACTOME_PEROXISOMAL_LIPID_METABOLISM"

## [1] "NUYTTEN_NIPP1_TARGETS_DN"

## [1] "BENPORATH_ES_CORE_NINE_CORRELATED"

## [1] "JI_RESPONSE_TO_FSH_DN"

## [1] "DORSAM_HOXA9_TARGETS_UP"

## [1] "PID_HDAC_CLASSI_PATHWAY"

## [1] "BIOCARTA_IGF1_PATHWAY"

## [1] "REACTOME_PROLONGED_ERK_ACTIVATION_EVENTS"

## [1] "PID_HDAC_CLASSII_PATHWAY"

## [1] "AMIT_SERUM_RESPONSE_120_MCF10A"

## [1] "WINTER_HYPOXIA_UP"

## [1] "DACOSTA_UV_RESPONSE_VIA_ERCC3_TTD_DN"

## [1] "BARIS_THYROID_CANCER_DN"

## [1] "LANDIS_ERBB2_BREAST_TUMORS_324_UP"

## [1] "SEIDEN_MET_SIGNALING"

## [1] "TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_DUCTAL_NORMAL_DN"

## [1] "REACTOME_SHC1_EVENTS_IN_ERBB4_SIGNALING"

## [1] "LEE_AGING_MUSCLE_DN"

## [1] "BIOCARTA_FMLP_PATHWAY"

## [1] "BIOCARTA_NGF_PATHWAY"

## [1] "REACTOME_ENOS_ACTIVATION_AND_REGULATION"

## [1] "GROSS_HYPOXIA_VIA_HIF1A_DN"

## [1] "STONER_ESOPHAGEAL_CARCINOGENESIS_UP"

## [1] "BIOCARTA_BCR_PATHWAY"

## [1] "PID_AVB3_OPN_PATHWAY"

## [1] "SA_B_CELL_RECEPTOR_COMPLEXES"

## [1] "PUIFFE_INVASION_INHIBITED_BY_ASCITES_UP"

## [1] "TRACEY_RESISTANCE_TO_IFNA2_DN"

## [1] "KAAB_FAILED_HEART_ATRIUM_DN"

## [1] "WANG_TUMOR_INVASIVENESS_DN"

## [1] "FORTSCHEGGER_PHF8_TARGETS_DN"

## [1] "SESTO_RESPONSE_TO_UV_C7"

## [1] "WANG_HCP_PROSTATE_CANCER"

## [1] "REACTOME_CTLA4_INHIBITORY_SIGNALING"

## [1] "KYNG_DNA_DAMAGE_BY_GAMMA_AND_UV_RADIATION"

## [1] "GOTZMANN_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_DN"